For example, when trying to integrate CCLE transcriptome and CCLE proteome data. In the corresponding BioplexAnalysis vignette (https://ccb-hms.github.io/BioPlexAnalysis/articles/TranscriptomeProteome.html#ccle-transcriptome-and-proteome-data-for-hct116-1), I am approaching this via AnnotationDbi::mapIds on the human orgdb package. One could either map the transcriptome data from ENSEMBL to ENTREZID or SYMBOL. Or map the proteome data from Uniprot to ENSEMBL. But I agree having the mapping annotated to the individual datasets will likely be handy.
For example, when trying to integrate CCLE transcriptome and CCLE proteome data. In the corresponding BioplexAnalysis vignette (https://ccb-hms.github.io/BioPlexAnalysis/articles/TranscriptomeProteome.html#ccle-transcriptome-and-proteome-data-for-hct116-1), I am approaching this via AnnotationDbi::mapIds on the human orgdb package. One could either map the transcriptome data from ENSEMBL to ENTREZID or SYMBOL. Or map the proteome data from Uniprot to ENSEMBL. But I agree having the mapping annotated to the individual datasets will likely be handy.